Figure 7

Induction of RNAPII-Ser5 (P) by 5-aza-CdR in intragenic loci is associated with activation of silenced genes. In panel (a), we show that while the majority of ChIP-seq peaks following 5-aza-CdR exposure already were present in the untreated cells, the majority of the 1,902 new peaks found map to intragenic loci (defined as the RefSeq gene annotation excluding the ±2 kb around the transcription start site, used to define the promoter). The new 1,306 intragenic peaks are found to decrease DNA methylation (increase HELP-tagging signal, panel (b)) and are associated with 519 genes, whose expression before (gray) and after (blue) 5-aza-CdR treatment is shown using a density plot (c). A decrease in the proportion of completely silenced genes (left peak) is observed in the genes gaining intragenic RNAPII-Ser5 (P), suggesting the activation of intragenic promoters. 5-aza-CdR, 5-aza-2′-deoxycytidine; RNAPII-Ser5 (P), serine 5-phosphorylated RNA polymerase II; FPKM, fragments per kilobase per million reads.h.